
Once the consensus map have been established, we can project all the observed QTL from the initial mapping experiments onto this consensus map. This is a compulsory step to carry out the meta-analysis.

To do so, use the program @code{QTLProj} as follows:

@cartouche
@example
$java org.metaqtl.main.QTLProj -m meta-map/consensus_map.xml \
                               -q xml -o meta-qtl/consensus --verbose
[ WARNING ] : Unable to project QTL Rebai_1997_SD_14 on chromosome 2
[ WARNING ] : Unable to project QTL Rebai_1997_SD_27 on chromosome 2
[ WARNING ] : Unable to project QTL Rebai_1997_SD_21 on chromosome 2
[ WARNING ] : Unable to project QTL Rebai_1997_SD_7 on chromosome 2
@end example
@end cartouche
@noindent

Note that setting the option @code{--verbose} displays the warnings. In this case, it seems that there is a problem with the mapping experiment @code{Rebai_1997} for the chromosome 2. Since here we focus on chromosome 1, we will ignore these warnings for the rest of the tutorial.

This command generates two files into the directory @file{meta-qtl}:
@itemize @bullet
@item @file{consensus_map.xml}: the consensus map plus the projected QTL.
@item @file{consensus_qtl.xml}: the consensus map with only the projected QTL.
@end itemize

Now, if we want to see how the QTL have been projected and are distributed along the chromosome 1, we can use the command @code{MapView} as follows:

@cartouche
@example
java org.metaqtl.main.MapView -m meta-qtl/consensus_map.xml -c 1 \
                              -o meta-qtl/images/consensus \
			      -p meta-qtl/images/consensus.par -q
@end example
@end cartouche
@noindent

This should give the following picture:

@float
@image{fig17,10cm,10cm,,}
@end float

Now, if we want to see the properties of the QTL projection for each QTL we can export the file @file{consensus_qtl.xml} into a flat text file using the command @code{Xml2A}:

@cartouche
@example
java org.metaqtl.main.Xml2A -x meta-qtl/consensus_qtl.xml\
                            -o meta-qtl/consensus_qtl.txt \
			    -t map -f tab
@end example
@end cartouche
@noindent

Thus we obtain the following list for the chromosome 1:

@float
@image{fig18,15cm,10cm,,}
@end float

The attributes @code{qtl.ci.from} and @code{qtl.ci.to} gives the new confidence interval of the QTL when a confidence interval exists in the intial mapping experiment. This new confidence interval is computed according to the projection scale given by the homothetic ratio gvien by the attribute @code{qtl.proj.mapScale}, while the position of the QTL is computed relatively to the flanking markers using the homothetic ratio given by the attribute @code{qtl.proj.intScale}. The boolean attributes @code{qtl.proj.shareFlanking} and @code{qtl.proj.swapFlanking} indicate for the former that the QTL flanking markers are observed into both the intial and the consensus map, and the later will be @code{true} if these markers are observed in a reverse order between the two maps.

Note that for half of the QTL in chromosome 1 there is no information about the CI. Nevertheless, if you look at the file @file{consensus_qtl.txt} you will see another field called @code{qtl.rsquare} which gives the percentage of variance explained by the QTL (this field was not included in the above table) and from which a theoretical confidence interval could be computed according to the mapping population properties (size and type of cross: these two parameters are given by the attributes @code{qtl.cross.size} and @code{qtl.cross.type}).
